Personnel
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
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Bibliography

Major publications by the team in recent years
[1]
M. Avalos, H. Pouyes, Y. Grandvalet, L. ORRIOLS, E. Lagarde.
Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm, in: BMC Bioinformatics, 2015, vol. 16, no Suppl 6, S1 p. [ DOI : 10.1186/1471-2105-16-S6-S1 ]
https://hal.inria.fr/hal-01217312
[2]
D. Commenges, A. Gégout-Petit.
The stochastic system approach for estimating dynamic treatments effect, in: Lifetime Data Analysis, 2015, 18 p. [ DOI : 10.1007/s10985-015-9322-3 ]
https://hal.inria.fr/hal-01205328
[3]
D. Commenges, H. Jacqmin-Gadda.
Dynamical Biostatistical Models, Chapman and Hall/CRC, October 2015.
https://hal.inria.fr/hal-01580149
[4]
B. P. Hejblum, J. Skinner, R. Thiébaut.
Time-Course Gene Set Analysis for Longitudinal Gene Expression Data, in: PLoS Computational Biology, 2015, vol. 11, no 6, e1004310 p. [ DOI : 10.1371/journal.pcbi.1004310 ]
https://hal.inria.fr/hal-01203446
[5]
C. C. Iwuji, J. Orne-Gliemann, J. Larmarange, N. Okesola, F. Tanser, R. Thiebaut, C. Rekacewicz, M.-L. Newell, F. Dabis, N. Low.
Uptake of Home-Based HIV Testing, Linkage to Care, and Community Attitudes about ART in Rural KwaZulu-Natal, South Africa: Descriptive Results from the First Phase of the ANRS 12249 TasP Cluster-Randomised Trial, in: PLoS Medicine, August 2016, vol. 13, no 8.
https://hal.inria.fr/hal-01406616
[6]
R. Le Grand, N. Dereuddre-Bosquet, S. Dispinseri, L. Gosse, D. Desjardins, X. Shen, M. Tolazzi, C. Ochsenbauer, H. Saidi, G. Tomaras, M. Prague, S. W. Barnett, R. Thiebaut, A. Cope, G. Scarlatti, R. J. Shattock, G. Silvestri.
Superior Efficacy of a Human Immunodeficiency Virus Vaccine Combined with Antiretroviral Prevention in Simian-Human Immunodeficiency Virus-Challenged Nonhuman Primates, in: Journal of Virology, May 2016, vol. 90, no 11, pp. 5315 - 5328.
https://hal.inria.fr/hal-01406364
[7]
E. Lhomme, L. Richert, Z. Moodie, C. Pasin, S. A. Kalams, C. Morgan, S. Self, S. C. De Rosa, R. Thiébaut.
Early CD4+ T Cell Responses Are Associated with Subsequent CD8+ T Cell Responses to an rAd5-Based Prophylactic Prime-Boost HIV Vaccine Strategy, in: PLoS ONE, April 2016, vol. 11, no 4.
https://hal.inria.fr/hal-01406611
[8]
B. Liquet, P. Lafaye De Micheaux, B. P. Hejblum, R. Thiébaut.
Group and sparse group partial least square approaches applied in genomics context, in: Bioinformatics, 2016, vol. 32, no 1, pp. 35-42. [ DOI : 10.1093/bioinformatics/btv535 ]
https://hal.inria.fr/hal-01288891
[9]
S. M. Moyo, T. M. Mohammed, K. M. Wirth, M. M. Prague, K. M. Bennett, M. P. Holme, L. M. Mupfumi, P. M. Sebogodi, N. M. Moraka, C. M. Boleo, C. M. Maphorisa, B. M. Seraise, S. M. Gaseitsiwe, R. M. Musonda, E. M. Van Widenfelt, K. M. Powis, T. M. Gaolathe, E. M. Tchetgen Tchetgen, J. M. Makhema, M. M. Essex, S. M. Lockman, V. M. Novitsky.
Point-of-Care Cepheid Xpert HIV-1 Viral Load Test in Rural African Communities Is Feasible and Reliable, in: Journal of Clinical Microbiology, 2016, vol. 54, no 12, pp. 3050 - 3055. [ DOI : 10.1128/JCM.01594-16 ]
https://hal.inria.fr/hal-01579540
[10]
F. Nakagawa, A. Van Sighem, R. Thiebaut, C. Smith, O. Ratmann, V. Cambiano, J. Albert, A. Amato-Gauci, D. Bezemer, C. Campbell, D. Commenges, M. Donoghoe, D. Ford, R. Kouyos, R. Lodwick, J. Lundgren, N. Pantazis, A. Pharris, C. Quinten, C. Thorne, G. Touloumi, V. Delpech, A. Phillips.
A method to estimate the size and characteristics of HIV-positive populations using an individual-based stochastic simulation model, in: Epidemiology, 2016, vol. 27, no 2, pp. 247-256. [ DOI : 10.1097/EDE.0000000000000423 ]
https://hal.inria.fr/hal-01288889
[11]
L. Richert, E. Lhomme, C. Fagard, Y. Levy, G. Chêne, R. Thiébaut.
Recent developments in clinical trial designs for HIV vaccine research, in: Human vaccines & immunotherapeutics, 2015, vol. 11, no 4, pp. 1022–9. [ DOI : 10.1080/21645515.2015.1011974 ]
https://hal.archives-ouvertes.fr/hal-01164644
[12]
P. Schommers, G. Martrus, U. Matschl, M. Sirignano, M. Lütgehetmann, L. Richert, T. J. Hope, G. Fätkenheuer, M. Altfeld, F. Kirchhoff.
Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations, in: Journal of Virology, July 2016, vol. 90, no 16, pp. 7579 - 7586. [ DOI : 10.1128/JVI.00867-16 ]
https://hal.archives-ouvertes.fr/hal-01404506
[13]
M. Surenaud, C. Manier, L. Richert, R. Thiébaut, Y. Levy, S. Hue, C. Lacabaratz.
Optimization and evaluation of Luminex performance with supernatants of antigen-stimulated peripheral blood mononuclear cells, in: BMC Immunology, December 2015, vol. 17, no 1, 44 p. [ DOI : 10.1186/s12865-016-0182-8 ]
http://www.hal.inserm.fr/inserm-01395760
[14]
R. Thiébaut, J. Drylewicz, M. Prague, C. Lacabaratz, S. Beq, A. Jarne, T. Croughs, R.-P. Sekaly, M. M. Lederman, I. Sereti, D. Commenges, Y. Lévy.
Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+ T Cells in HIV-1 Infection, in: PLoS computational biology, 2014, vol. 10, no 5, e1003630.
[15]
R. Thiébaut, A. Jarne, J.-P. Routy, I. Sereti, M. Fischl, P. Ive, R. F. Speck, G. D'Offizi, S. Casari, D. Commenges, S. Foulkes, V. Natarajan, T. Croughs, J.-F. Delfraissy, G. Tambussi, Y. Levy, M. M. Lederman.
Repeated Cycles of Recombinant Human Interleukin 7 in HIV-Infected Patients With Low CD4 T-Cell Reconstitution on Antiretroviral Therapy: Results of 2 Phase II Multicenter Studies, in: Clinical Infectious Diseases, May 2016, vol. 62, no 9, pp. 1178 - 1185.
https://hal.inria.fr/hal-01406362
Publications of the year

Articles in International Peer-Reviewed Journals

[16]
D. Agniel, B. P. Hejblum.
Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, in: Biostatistics, 2017, vol. 18, no 4, pp. 589-604, https://arxiv.org/abs/1605.02351. [ DOI : 10.1093/biostatistics/kxx005 ]
https://hal.inria.fr/hal-01579077
[17]
V. Bouteloup, C. Sabin, A. Mocroft, L. Gras, N. Pantazis, V. Le Moing, A. D'Arminio Monforte, M. Mary-Krause, R. Roca, J. M. Miro, M. Battegay, N. H. Brockmeyer, M. Berenguer, P. Morlat, C. Obel, S. De Wit, G. Fätkenheuer, R. Zangerle, J. Ghosn, R. Pérez-Hoyos, M. Campbell, C. Prins, G. Chêne, L. Meyer, M. Dorrucci, C. Torti, R. Thiébaut.
Reference curves for CD4 T-cell count response to combination antiretroviral therapy in HIV-1-infected treatment-naïve patients, in: HIV Medicine, 2017, vol. 18, no 1, pp. 33 - 44. [ DOI : 10.1111/hiv.12389 ]
https://hal.archives-ouvertes.fr/hal-01579158
[18]
R. Genuer, J.-M. Poggi, C. Tuleau-Malot, N. Villa-Vialaneix.
Random Forests for Big Data, in: Big Data Research, September 2017, vol. 9, pp. 28-46, https://arxiv.org/abs/1511.08327. [ DOI : 10.1016/j.bdr.2017.07.003 ]
https://hal.archives-ouvertes.fr/hal-01233923
[19]
B. P. Hejblum, J. Cui, L. J. Lahey, A. Cagan, J. A. Sparks, J. Sokolove, T. Cai, K. P. Liao.
Association between anti-citrullinated fibrinogen antibodies and coronary artery disease in rheumatoid arthritis, in: Arthritis Care & Research, 2017, forthcoming. [ DOI : 10.1002/acr.23444 ]
https://hal.inria.fr/hal-01654403
[20]
P. Hellard, C. Scordia, M. F. Avalos, I. Mujika, P. David.
Modelling of optimal training load patterns during the 11 weeks preceding major competition in elite swimmers, in: Applied Physiology, Nutrition, and Metabolism, 2017.
https://hal.inria.fr/hal-01577936
[21]
A. Jarne, D. Commenges, M. Prague, Y. Levy, R. Thiébaut.
Modeling CD4 + T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7, in: Annals Of Applied Statistics, June 2017.
https://hal.inria.fr/hal-01579008
[22]
K. Liao, J. A. Sparks, B. P. Hejblum, I.-H. Kuo, J. Cui, L. J. Lahey, A. Cagan, V. S. Gainer, W. Liu, T. T. Cai, J. Sokolove, T. Cai.
Phenome-Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis, in: Arthritis & rheumatology, April 2017, vol. 69, no 4, pp. 742 - 749. [ DOI : 10.1002/art.39974 ]
https://hal.inria.fr/hal-01654405
[23]
F. Mougin, D. Auber, R. Bourqui, G. Diallo, I. Dutour, V. Jouhet, F. Thiessard, R. Thiebaut, P. Thebault.
Visualizing omics and clinical data: which challenges for dealing with their variety?, in: Methods, 2017. [ DOI : 10.1016/j.ymeth.2017.08.012 ]
https://hal.archives-ouvertes.fr/hal-01671067
[24]
N. Mélanie, M. F. Avalos, A. LUXCEY, B. Contrand, L. R. Salmi, A. Fourrier-Reglat, B. Gadegbeku, E. Lagarde, L. ORRIOLS.
Prescription medicine use by pedestrians and the risk of injurious road traffic crashes: A case-crossover study, in: PLoS Medicine, 2017.
https://hal.inria.fr/hal-01577941
[25]
M.-Q. Picat, I. Pellegrin, J. Bitard, L. Wittkop, C. Proust-Lima, B. Liquet, J.-F. Moreau, F. Bonnet, P. Blanco, R. Thiébaut.
Integrative Analysis of Immunological Data to Explore Chronic Immune T-Cell Activation in Successfully Treated HIV Patients, in: PLoS ONE, January 2017, vol. 12, no 1. [ DOI : 10.1371/journal.pone.0169164 ]
https://hal.archives-ouvertes.fr/hal-01579159
[26]
M. Prague, D. Commenges, J. M. Gran, B. Ledergerber, J. Young, H. Furrer, R. Thiébaut.
Dynamic models for estimating the effect of HAART on CD4 in observational studies: Application to the Aquitaine Cohort and the Swiss HIV Cohort Study, in: Biometrics, March 2017, vol. 73, no 1, pp. 294 - 304. [ DOI : 10.1111/biom.12564 ]
https://hal.inria.fr/hal-01670680
[27]
M. Prague, E. Turner, l. Fan, G. John, M. David.
Review of recent Methodological Developments in group-randomized trials: Part 1 - Design, in: American Journal of Public Health, June 2017.
https://hal.inria.fr/hal-01579073
[28]
M. Prague, E. Turner, G. John, l. Fan, M. David.
Review of recent Methodological Developments in group-randomized trials: Part 2 - Analysis, in: American Journal of Public Health, June 2017.
https://hal.inria.fr/hal-01579075
[29]
M. Prague, R. Wang, V. de Gruttola.
CRTgeeDR: An R Package for Doubly Robust Generalized Estimating Equations Estimations in Cluster Randomized Trials with Missing Data, in: R journal, September 2017.
https://hal.inria.fr/hal-01579080
[30]
A. Rechtien, L. Richert, H. Lorenzo, G. Martrus, B. P. Hejblum, C. Dahlke, R. Kasonta, M. Zinser, H. Stubbe, U. Matschl, A. Lohse, V. Krähling, M. Eickmann, S. Becker, R. Thiébaut, M. Altfeld, M. Addo.
Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV, in: Cell Reports , 2017, vol. 20, no 9, pp. 2251 - 2261. [ DOI : 10.1016/j.celrep.2017.08.023 ]
https://hal.inria.fr/hal-01579246
[31]
M. Tabue-Teguo, L. Grasset, J. A. Avila-Funes, R. Genuer, C. Proust-Lima, K. Pérès, C. Feart, H. Amieva, M. G.-C. Harmand, C. Helmer, N. Salles, M. Rainfray, J. F. Dartigues.
Prevalence and Co-Occurrence of Geriatric Syndromes in People Aged 75 Years and Older in France: Results From the Bordeaux Three-city Study, in: Journals of Gerontology, Series A, May 2017. [ DOI : 10.1093/gerona/glx068 ]
https://hal.inria.fr/hal-01652204
[32]
R. Thiebaut, S. Hue, F. Le Marec, J.-D. Lelievre, M. Dupon, E. Foucat, E. Lazaro, F. Dabis, P. Duffau, L. Wittkop, M. Surenaud, I. Pellegrin, C. Lacabaratz, F. Bonnet, Y. Lévy.
Serum ST2 level is an independent predictor of all-cause mortality in HIV-infected patients. Aquitaine Cohort, France, in: AIDS, 2017.
https://hal.archives-ouvertes.fr/hal-01671081
[33]
R. Thiebaut, F. Thiessard.
Public Health and Epidemiology Informatics, in: IMIA Yearbook of Medical Informatics, 2017. [ DOI : 10.15265/IY-2017-035 ]
https://hal.archives-ouvertes.fr/hal-01671095
[34]
L. Zago, P.-Y. Hervé, R. Genuer, A. Laurent, B. Mazoyer, N. Tzourio-Mazoyer, M. Joliot.
Predicting hemispheric dominance for language production in healthy individuals using support vector machine, in: Human Brain Mapping, September 2017. [ DOI : 10.1002/hbm.23770 ]
https://hal.inria.fr/hal-01590497

National Conferences with Proceedings

[35]
M. Prague, R. Thiébaut, P. Moireau, A. Collin.
Joint-state and parameters estimation using nudging and SEIK filters for HIV mechanistic models, in: Journée de la statistique francaise, Avignon, France, June 2017.
https://hal.inria.fr/hal-01579068

Conferences without Proceedings

[36]
H. Lorenzo, R. Thiebaut, J. Saracco.
Multi-block high-dimensional lasso-penalized analysis with imputation of missing data applied to postgenomic data in an Ebola vaccine trial, in: Annual workshop on Statistical Methods for Post Genomic Data - SMPGD 2018, Montpellier, France, January 2018.
https://hal.archives-ouvertes.fr/hal-01664610
[37]
P. Soret, M. F. Avalos, S. Cheng, R. Thiebaut.
High-dimensional compositional microbiota data: state-of-the-art of methods and software implementations, in: 2017 - GDR « Statistiques et santé », Bordeaux, France, October 2017.
https://hal.inria.fr/hal-01667295

Other Publications

[38]
R. Genuer, J.-M. Poggi.
Arbres CART et Forêts aléatoires,Importance et sélection de variables, January 2017, working paper or preprint.
https://hal.archives-ouvertes.fr/hal-01387654
[39]
B. P. Hejblum, C. Alkhassim, R. Gottardo, F. Caron, R. Thiébaut.
Sequential Dirichlet Process Mixtures of Multivariate Skew t-distributions for Model-based Clustering of Flow Cytometry Data, August 2017, https://arxiv.org/abs/1702.04407 - 39 pages, 11 figures.
https://hal.inria.fr/hal-01579063
[40]
M. ´. Prague, D. Commenges, R. Thiébaut.
In Silico Evaluation of HIV Short-cycle Therapies with Dynamical Models, August 2017, Keystone Symposium , Poster.
https://hal.inria.fr/hal-01579070
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